diyspartanbiotechhttps://diyspartanbiotech.wordpress.com
The sky is not the limit
Sun, 18 Nov 2018 04:46:47 +0000 en
hourly
1 http://wordpress.com/https://s0.wp.com/i/buttonw-com.pngdiyspartanbiotechhttps://diyspartanbiotech.wordpress.com
Pics of plant tissue culture, micropropagationhttps://diyspartanbiotech.wordpress.com/2018/07/02/pics-of-plant-tissue-culture-micropropagation/
https://diyspartanbiotech.wordpress.com/2018/07/02/pics-of-plant-tissue-culture-micropropagation/#commentsMon, 02 Jul 2018 16:22:12 +0000http://diyspartanbiotech.wordpress.com/?p=467Continue reading →]]>I noticed that there are hardly any pictures on Google Images so I thought putting these here would enrich the internet. I made them with my phone so it’s not best quality but they are free to be used anywhere

It starts as a tiny piece of the leaf that has been surface sterilized 30 secs wih Ethanol (70%) and then 3 mins in 35% dilution of houshold bleach. subsequently washed twice with autoclaved water to remove bleach. You can see how they have developed after 3 weeks

“Genetic modification is unnatural.” That phrase is very common. However, if you look at two apple trees in nature, their DNA will differ a bunch. During sexual breeding, roughly half of the DNA of father and half of the mother plant will be recombined. Random recombination, homologous recombination, ancient retroviruses, transposons (jumping genes) and retrotransposons will scramble up the genome. The polymerase will make copying errors such as inserting the wrong letter (ATGA->ACGA) and sometimes leave large deletions or duplications in the DNA. Also, the fact that this is natural doesn’t mean it’s harmless. Just google for the Lenape potato or the killer zucchini, natural breeding can and does produce toxic and dangerous varieties.

“But these are all natural. If humans put a gene from a fish into a tomato, that’s somehow different!” Sounds legit, right? Just in the recent years we have seen the prices for sequencing DNA drop drastically (reading DNA), and guess what we found. There’s genes from lots of different animals and plants in many different animals and plants. Google “horizontal gene transfer”, the results will blow your mind! Just to give a few examples: a fern that acquired a moss gene, butterflies that acquired wasp genes, in humans we have found more than 100 bacterial genes, … Even mammalian sperm produces reverse transcriptse and can take up RNA and DNA from its environment. In bacteria, species barriers have been known to be randomly defined by man for a long time.

“In Europe we have banned GMOs, so we have natural crops.” Nothing could be further away from the truth. As GMOs have been outlawed but “random breeding methods” are exempt from these regulations, breeders use older methods such as creating mutants by employing mutagenic chemicals and radioactive radiation. Instead of just adding one known and characterized gene, you randomly mutate hundreds of genes at the same time and pick the mutant that makes the biggest fruits. Side effects? There’s no way to tell, as no safety testing is required by law, unlike with genetically engineered plants that take 10-15 years of studies for approval which cost around 100 million dollars per plant.

“GMOs are all patented and inherently used for profit” While it is true that GMOs can (but don’t have to – check out the humanitarian open source Golden Rice) be patented, this is mainly caused by the expensive process to get them through FDA approval. You cannot sell it for 15 years, so companies patent it to make it more likely that their investment will come back with interests. Also, small Universities or entities cannot afford FDA approval processes and thus big companies like Monsanto can have big market share and less competition.

]]>https://diyspartanbiotech.wordpress.com/2017/02/08/428/feed/0diyspartanbiotechPromoters of the day – EF1ahttps://diyspartanbiotech.wordpress.com/2017/02/04/promoters-of-the-day-ef1a/
https://diyspartanbiotech.wordpress.com/2017/02/04/promoters-of-the-day-ef1a/#respondSat, 04 Feb 2017 15:37:55 +0000http://diyspartanbiotech.wordpress.com/?p=424Continue reading →]]>EF1a – a „strong“ native mammalian promoter active in most or all tissues. Not as strong as viral promoters like CMV. Tends not to get silenced (like CMV does). Sometimes the EF1a core promoter with CMV enhancer is used.

Citing Invivogen “The EF-1 alpha gene encodes for elongation factor-1 alpha which is one of the most abundant proteins in eukaryotic cells and is expressed in almost all kinds of mammalian cells. The promoter of this “housekeeping” gene exhibits a strong activity, higher than viral promoters such as SV40 and RSV promoters1 , and on the contrary to the CMV promoter, yields persistent expression of the transgene in vivo2 . The rat EF-1α promoter shares a 45.05% homology to the human EF-1α promoter.” ( http://www.yrgene.com/documents/promoter/pdrive-ref1a_tds.pdf )

]]>https://diyspartanbiotech.wordpress.com/2017/02/04/promoters-of-the-day-ef1a/feed/0diyspartanbiotechSequence Repositoryhttps://diyspartanbiotech.wordpress.com/2017/01/29/sequence-repository/
https://diyspartanbiotech.wordpress.com/2017/01/29/sequence-repository/#respondSun, 29 Jan 2017 19:58:06 +0000http://diyspartanbiotech.wordpress.com/?p=408Continue reading →]]>Just found this. A ribozyme that cleaves itself, unless it binds tetracyclin. Proven to work in mammalian cells.
You just have to embedd this ribozyme into a mRNA, ideally direcly after the stop codon (3’UTR). CAAA3 is used as a spacer so the ribozyme folding is more smooth, presumably because A-T binding is a lot weaker than G-C.
Seems to be very helpful when you want to use tetracycline to activate gene expression but you don’t want to introduce foreign proteins (such as the tet-transcativator that then binds a tet-operator-CMV Promoter). Without tetracycline in the medium, the mRNA cleaves itself and you get only ~25% of the expression because mRNA without a polyA tail is rapidly degraded. When you add 50 uM tet, the ribozyme is prevented from cutting itself and you get the full expression.

The ribozyme is described in the study “Conditional Control of Mammalian Gene Expression by Tetracycline-Dependent Hammerhead Ribozymes” by Kim Beilstein, Alexander Wittmann, Manuel Grez, and Beatrix Suess. I had ty type it in from the graphic, always annowing when the full sequence isn’t given in a format that’s copyable.

Alledgedly there is a better ribozyme from the study “Rational design of aptazyme riboswitches for efficient control of gene expression in mammlian cells” that has 20 fold repression wiothout tetracyclin. Unfortunately they hid their sequence very well in the paper and I have to reverse engineer all of their paper to find the sequence they used. #moretransparencyinqualityjournalsplease

EDIT: The author of “Rational design of aptazyme riboswitches for efficient control of gene expression in mammlian cells” has kindly replied to my email the next day. He provided the sequences:

I shovel telomeres for a living. My friends in the computer industry are always asking me: ‘Why can’t you biotech guys cure cancer? Or aging? Or the common cold? What do you do with all those billions of government research dollars?’

Well, it’s time to confess: Biologists bought three stuffed mice and two petri dishes in 1974. These are recycled in staged publicity photos in such high-profile popular glossies as Proceedings of the National Academy of Sciences, Cell, and Eur J Gastroenterol Hepatol. Our much-hyped ‘gene sequencing,’ ‘chromosome imaging,’ etc. are all done on Photoshop by companies in Taipei . All the rest of the money goes to yachts, scuba equipment, and private islands in Fiji for all postdocs and research associates. That’s why medical researchers always look so tanned and vigorous.

OK, seriously: If the computer industry were running under the same conditions as biotech, this is how it would work:

There would be a Federal Data Administration (FDA). Every processor, peripheral, program, printer, and power cord made in or imported into the USA would have to obtain FDA approval. This would require an average of 19 years of safety testing on lab rats and clinical trials for effectiveness on nerd volunteers with informed consent, before prescription for general human use is allowed. Any change of any kind to any chip, ergonomic keyboard, or line of code would require re-approval of the entire system and any hardware or software that could in principle be connected to it via Internet, intranet, or hand-carried disk.

In the medical system, this sort of approval can be done for only a bit over $802 million per drug or medical device (Tufts study, 2001). So it might cost only a few times more when applied to a global industry producing next-generation silicon chips. Anyway, how can anyone put a price tag on safety? Think of the children!

Today even someone who dropped out of college could legally own a large software company. To remedy this unconscionable state of affairs, state licensing boards would be created to require American Mainframe Association (AMA) membership for all computer professionals. This would ensure that all programmers go to college and postgraduate school for at least eight years, and then serve multi-year nerdships and residencies before being allowed to practice independently. Thus programmers would be fully prepared to start writing BASIC programs by age 28-30, and attain full professional status by their 40s.

These AMA professionals would prescribe for consumers the ‘right’ hardware and software (within the prescribing and cost limits of the appropriate HMO, see below). To guard against improper (‘recreational’) use of computers, all information products would now require a prescription from a professional.

A Data Enforcement Agency (DEA) would be empowered under the asset forfeiture laws to confiscate the property of smugglers and users of illegal data processing paraphernalia, such as that used in so-called ‘video games’ or ‘palm pilots.’ The DEA would also have the responsibility of ensuring that no unapproved data flows in or out of our borders.

Then the IRS would make buying computers for the home use of employees a deductible expense for employers (but not for employees), as is true of health insurance today. Companies would be forced to buy computers for their employees through Hardware Maintenance Organizations (HMOs), instead of allowing the employees to buy them directly.

Finally, the Federal government would hire hundreds of thousands of programmers and chip designers to work in government-run ‘computer research,’ controlled by NIH, the various armed services, and other fountains of innovation. Private ‘cybertech’ companies could have whoever was left over . . . if they could figure out how to con investors into funding companies which were rarely allowed to sell their products.

If we had really let government run the computer industry this way, there would be no Intel, IBM or Apple. There would be no chip industry. There would be no Internet. The NIH would be funding hundreds of labs to develop better vacuum tubes.

Now, all you programmers who are snickering at the poor dumb biologists: let me point out something. You, personally, aren’t made of doped silicon. You are made of DNA and some other junk banging around inside lipid bilayers. If you want to improve your life in any meaningful way, you need to be able to buy stuff to upgrade your DNA system.

Some organisms, like Bowhead whales, already manage to make DNA systems work for over 200 years. That means their cancer control is 1,000 times as good as ours (twice the lifespan times 500 times the cell number), and their aging control is at least twice as good. A real free-market biotech industry could pirate these already-existing DNA programs and sell them to you cheap (whales don’t get royalties, and DNA replicates as easily as chips do).

So, since you computer guys have all the money, it would behoove you to use a little of it to get rid of the FDA and all the rest of the medieval guild nonsense that encrusts the biotech industry. Then you would finally see some progress against cancer and aging.

Oh, the common cold? We could wipe out the existing varieties, but RNA and DNA hackers will always resequence new types. Viruses will always be with us; you just have to continuously update your immune system’s definitions. “